Document Detail


Prokaryotic regulatory systems biology: Common principles governing the functional architectures of Bacillus subtilis and Escherichia coli unveiled by the natural decomposition approach.
MedLine Citation:
PMID:  22728391     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Escherichia coli and Bacillus subtilis are two of the best-studied prokaryotic model organisms. Previous analyses of their transcriptional regulatory networks have shown that they exhibit high plasticity during evolution and suggested that both converge to scale-free-like structures. Nevertheless, beyond this suggestion, no analyses have been carried out to identify the common systems-level components and principles governing these organisms. Here we show that these two phylogenetically distant organisms follow a set of common novel biologically consistent systems principles revealed by the mathematically and biologically founded natural decomposition approach. The discovered common functional architecture is a diamond-shaped, matryoshka-like, three-layer (coordination, processing, and integration) hierarchy exhibiting feedback, which is shaped by four systems-level components: global transcription factors (global TFs), locally autonomous modules, basal machinery and intermodular genes. The first mathematical criterion to identify global TFs, the κ-value, was reassessed on B. subtilis and confirmed its high predictive power by identifying all the previously reported, plus three potential, master regulators and eight sigma factors. The functional conserved cores of modules, basal cell machinery, and a set of non-orthologous common physiological global responses were identified via both orthologous genes and non-orthologous conserved functions. This study reveals novel common systems principles maintained between two phylogenetically distant organisms and provides a comparison of their lifestyle adaptations. Our results shed new light on the systems-level principles and the fundamental functions required by bacteria to sustain life.
Authors:
Julio A Freyre-González; Luis G Treviño-Quintanilla; Ilse A Valtierra-Gutiérrez; Rosa María Gutiérrez-Ríos; José A Alonso-Pavón
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-6-20
Journal Detail:
Title:  Journal of biotechnology     Volume:  -     ISSN:  1873-4863     ISO Abbreviation:  -     Publication Date:  2012 Jun 
Date Detail:
Created Date:  2012-6-25     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8411927     Medline TA:  J Biotechnol     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2012. Published by Elsevier B.V.
Affiliation:
Department of Molecular Microbiology, Institute for Biotechnology, Universidad Nacional Autónoma de México. Apdo. Postal 510-3, 62250. Cuernavaca, Morelos, México; Undergraduate Program on Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México. Av. Universidad s/n, Col. Chamilpa, 62210. Cuernavaca, Morelos, México.
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